{"id":6637,"date":"2021-07-26T10:45:08","date_gmt":"2021-07-26T10:45:08","guid":{"rendered":"https:\/\/rhizorna.sombradoble.es\/?page_id=6637"},"modified":"2021-12-13T12:29:58","modified_gmt":"2021-12-13T12:29:58","slug":"research","status":"publish","type":"page","link":"https:\/\/grupos.eez.csic.es\/rhizorna\/research\/","title":{"rendered":"Research"},"content":{"rendered":"[vc_row type=\u00bbin_container\u00bb full_screen_row_position=\u00bbmiddle\u00bb column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb scene_position=\u00bbcenter\u00bb text_color=\u00bbdark\u00bb text_align=\u00bbleft\u00bb row_border_radius=\u00bbnone\u00bb row_border_radius_applies=\u00bbbg\u00bb overlay_strength=\u00bb0.3&#8243; gradient_direction=\u00bbleft_to_right\u00bb shape_divider_position=\u00bbbottom\u00bb bg_image_animation=\u00bbnone\u00bb][vc_column column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bbdefault\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb tablet_text_alignment=\u00bbdefault\u00bb phone_text_alignment=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb]<style type=\"text\/css\">@media only screen and (min-width: 1300px) { #nectar-slider-instance-1, #nectar-slider-instance-1 .swiper-container { height: 280px; }  } @media only screen and (max-width: 1299px) { #nectar-slider-instance-1, #nectar-slider-instance-1 .swiper-container { height: 233.33333333333px; }  } @media only screen and (max-width: 1000px) { #nectar-slider-instance-1, #nectar-slider-instance-1 .swiper-container { height: 200px; }  } @media only screen and (max-width: 690px) { #nectar-slider-instance-1, #nectar-slider-instance-1 .swiper-container { height: 103.7037037037px; }  } <\/style><div  data-transition=\"slide\" data-overall_style=\"classic\" data-flexible-height=\"\" data-animate-in-effect=\"zoom-out\" data-fullscreen=\"false\" data-button-sizing=\"regular\" data-button-styling=\"btn_with_count\" data-autorotate=\"\" data-parallax=\"false\" data-parallax-disable-mobile=\"\" data-caption-trans=\"fade_in_from_bottom\" data-parallax-style=\"bg_only\" data-bg-animation=\"none\" data-full-width=\"true\" class=\"nectar-slider-wrap \" id=\"nectar-slider-instance-1\"><div class=\"swiper-container\"  data-tho=\"auto\" data-tco=\"auto\" data-pho=\"auto\" data-pco=\"auto\" data-loop=\"false\" data-height=\"280\" data-min-height=\"\" data-arrows=\"false\" data-bullets=\"false\" data-bullet_style=\"see_through\" data-bullet_position=\"bottom\" data-desktop-swipe=\"false\" data-settings=\"\"> <div class=\"swiper-wrapper\"><div class=\"swiper-slide\" data-desktop-content-width=\"auto\" data-tablet-content-width=\"auto\" data-bg-alignment=\"center\" data-color-scheme=\"light\" data-x-pos=\"centered\" data-y-pos=\"middle\" ><div class=\"slide-bg-wrap\"><div class=\"image-bg\" style=\"background-image: url(https:\/\/grupos.eez.csic.es\/rhizorna\/\/wp-content\/uploads\/2021\/10\/leaf-abstract-PSXECSA-scaled.jpg);\"> &nbsp; <\/div><div class=\"slide-bg-overlay\" style=\"background-color: #3e8932;\"> &nbsp; <\/div><\/div><div class=\"container\">\r\n\t\t\t\t\t\t<div class=\"content\"><h2>RESEARCH<\/h2><\/div>\r\n\t\t\t\t\t\t\t\t<\/div><!--\/container--><div class=\"video-texture active_texture\"> <span class=\"ie-fix\"><\/span> <\/div><\/div> <!--\/swiper-slide--><\/div><div class=\"nectar-slider-loading \"> <span class=\"loading-icon none\">   <\/span> <\/div> <\/div> \r\n\t\t\t\t\t\r\n\t\t\t\t\t<\/div>[\/vc_column][\/vc_row][vc_row type=\u00bbfull_width_background\u00bb full_screen_row_position=\u00bbmiddle\u00bb column_margin=\u00bb90px\u00bb equal_height=\u00bbyes\u00bb content_placement=\u00bbmiddle\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbcolumn_reverse\u00bb column_direction_phone=\u00bbcolumn_reverse\u00bb bg_color=\u00bb#ffffff\u00bb scene_position=\u00bbcenter\u00bb top_padding=\u00bb6%\u00bb bottom_padding=\u00bb2%\u00bb top_padding_tablet=\u00bb8%\u00bb bottom_padding_tablet=\u00bb8%\u00bb text_color=\u00bbdark\u00bb text_align=\u00bbleft\u00bb row_border_radius=\u00bbnone\u00bb row_border_radius_applies=\u00bbbg\u00bb id=\u00bbhome\u00bb overlay_strength=\u00bb0.5&#8243; gradient_direction=\u00bbtop_to_bottom\u00bb shape_divider_position=\u00bbbottom\u00bb bg_image_animation=\u00bbnone\u00bb shape_type=\u00bbstraight_section\u00bb][vc_column column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bbdefault\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.5&#8243; width=\u00bb1\/2&#8243; tablet_width_inherit=\u00bbdefault\u00bb tablet_text_alignment=\u00bbdefault\u00bb phone_text_alignment=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb offset=\u00bbvc_col-xs-12&#8243;][vc_row_inner column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb text_align=\u00bbleft\u00bb][vc_column_inner column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bbdefault\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.5&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb parallax_bg=\u00bbtrue\u00bb parallax_bg_speed=\u00bbfast\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb][image_with_animation image_url=\u00bb6699&#8243; animation=\u00bbFade In\u00bb hover_animation=\u00bbnone\u00bb alignment=\u00bb\u00bb border_radius=\u00bbnone\u00bb box_shadow=\u00bbnone\u00bb image_loading=\u00bbdefault\u00bb max_width=\u00bb100%\u00bb max_width_mobile=\u00bbdefault\u00bb][\/vc_column_inner][\/vc_row_inner][\/vc_column][vc_column column_padding=\u00bbpadding-4-percent\u00bb column_padding_tablet=\u00bbno-extra-padding\u00bb column_padding_phone=\u00bbno-extra-padding\u00bb column_padding_position=\u00bbright\u00bb column_element_spacing=\u00bb10px\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb zindex=\u00bb100&#8243; gradient_direction=\u00bbleft_t_to_right_b\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/2&#8243; tablet_width_inherit=\u00bbdefault\u00bb tablet_text_alignment=\u00bbdefault\u00bb phone_text_alignment=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb offset=\u00bbvc_col-xs-12&#8243;][vc_row_inner column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb text_align=\u00bbleft\u00bb min_width=\u00bb47vh\u00bb][vc_column_inner column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bb5px\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb enable_animation=\u00bbtrue\u00bb animation=\u00bbfade-in-from-bottom\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb enable_border_animation=\u00bbtrue\u00bb][nectar_highlighted_text color_type=\u00bbregular\u00bb highlight_color=\u00bb#3e8932&#8243; text_color=\u00bb#3e8932&#8243; style=\u00bbregular_underline\u00bb highlight_expansion=\u00bbdefault\u00bb underline_thickness=\u00bb1px\u00bb delay=\u00bb400&#8243;]\n<h5><em>Regulation by RNA in Rhizobia<\/em><\/h5>\n[\/nectar_highlighted_text][\/vc_column_inner][\/vc_row_inner][vc_row_inner column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb text_align=\u00bbleft\u00bb min_width=\u00bb47vh\u00bb][vc_column_inner column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bb5px\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb enable_animation=\u00bbtrue\u00bb animation=\u00bbfade-in-from-bottom\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb enable_border_animation=\u00bbtrue\u00bb][vc_column_text]\n<p style=\"text-align: justify;\">High throughput RNA sequencing (RNA-seq) has unveiled unexpectedly complex transcriptional outputs in bacteria, adding large and heterogeneous inventories of small non-protein coding transcripts (sRNAs) to the translation-related ribosomal (rRNA), transfer (tRNA) and messenger (mRNA) RNAs. Most sRNAs act as post-transcriptional regulators of gene expression, governing extensive regulatory networks that help bacteria cope with and adapt to changing environments. However, sRNAs are systematically overlooked in the annotation of bacterial genomes and riboregulation remains understudied in most environmentally relevant non-classical model microbes.<\/p>\n[\/vc_column_text][\/vc_column_inner][\/vc_row_inner][\/vc_column][\/vc_row][vc_row type=\u00bbfull_width_background\u00bb full_screen_row_position=\u00bbmiddle\u00bb column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb bg_color=\u00bb#ffffff\u00bb scene_position=\u00bbcenter\u00bb bottom_padding=\u00bb6%\u00bb text_color=\u00bbdark\u00bb text_align=\u00bbleft\u00bb row_border_radius=\u00bbnone\u00bb row_border_radius_applies=\u00bbbg\u00bb overlay_strength=\u00bb0.3&#8243; gradient_direction=\u00bbleft_to_right\u00bb shape_divider_position=\u00bbbottom\u00bb bg_image_animation=\u00bbnone\u00bb shape_type=\u00bb\u00bb][vc_column column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bbdefault\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb tablet_text_alignment=\u00bbdefault\u00bb phone_text_alignment=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb][vc_column_text]\n<p style=\"text-align: justify;\">In the RhizoRNA Lab we study RNA regulation in a group of \u03b1-proteobacteria, known as rhizobia, that establish nitrogen-fixing endosymbioses with legume plants. These mutualistic associations render plant growth independent of environmentally unfriendly chemical fertilizers and are, therefore, pillars of planet sustainability. Besides, rhizobia-legume symbioses provide invaluable experimental systems for deciphering the adaptive traits operating in bacteria during chronic infection of eukaryotic hosts. Rhizobia persist in soil under usually harsh conditions, actively compete in the rhizosphere with beneficial and pathogenic microorganisms, and finally induce the host plant to form root nodules that accommodate nitrogen-fixing differentiated bacteroids intracellularly. During this symbiotic transition rhizobial gene expression undergoes continuous and profound reprograming in response to abiotic stimuli and plant-derived cues. We are interested in unravelling the roles of sRNAs in these adaptive regulatory networks and their impact in rhizobial physiology, metabolism and symbiotic nitrogen-fixation. Given that RNA regulation relies mostly on modifiable base-pairing interactions, our longer-term goal is to exploit the functional plasticity of sRNAs for the engineering of the legumes rhizobiome and symbiotic efficiency of rhizobia in the sustainable agricultural practice.<\/p>\n[\/vc_column_text][\/vc_column][\/vc_row][vc_row type=\u00bbfull_width_background\u00bb full_screen_row_position=\u00bbmiddle\u00bb column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb bg_color=\u00bb#ffffff\u00bb scene_position=\u00bbcenter\u00bb text_color=\u00bbdark\u00bb text_align=\u00bbleft\u00bb row_border_radius=\u00bbnone\u00bb row_border_radius_applies=\u00bbbg\u00bb overlay_strength=\u00bb0.3&#8243; gradient_direction=\u00bbleft_to_right\u00bb shape_divider_position=\u00bbbottom\u00bb bg_image_animation=\u00bbnone\u00bb shape_type=\u00bb\u00bb][vc_column column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bbdefault\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb tablet_text_alignment=\u00bbdefault\u00bb phone_text_alignment=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb][page_submenu alignment=\u00bbcenter\u00bb sticky=\u00bbtrue\u00bb bg_color=\u00bb#2c671f\u00bb link_color=\u00bb#ffffff\u00bb][page_link link_url=\u00bb#researchlines\u00bb title=\u00bbResearch Lines\u00bb id=\u00bb1639398352701-0&#8243; tab_id=\u00bb1639398352702-6&#8243;] [\/page_link][page_link link_url=\u00bb#methodological\u00bb title=\u00bbMethodological approaches\u00bb id=\u00bb1639398352738-6&#8243; tab_id=\u00bb1639398352738-0&#8243;] [\/page_link][\/page_submenu][vc_row_inner column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb text_align=\u00bbleft\u00bb][vc_column_inner column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bbdefault\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb][vc_column_text]\n<h3 style=\"text-align: center;\"><span style=\"color: #3e8932;\">Research Lines<\/span><\/h3>\n[\/vc_column_text][divider line_type=\u00bbSmall Line\u00bb line_alignment=\u00bbcenter\u00bb line_thickness=\u00bb1&#8243; divider_color=\u00bbaccent-color\u00bb animate=\u00bbyes\u00bb][\/vc_column_inner][\/vc_row_inner][vc_row_inner equal_height=\u00bbyes\u00bb content_placement=\u00bbmiddle\u00bb column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb text_align=\u00bbleft\u00bb el_id=\u00bbresearchlines\u00bb][vc_column_inner column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bbdefault\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb][vc_column_text]<strong>1. Structure of the rhizobial non-coding transcriptome.<\/strong><\/p>\n<p style=\"text-align: justify;\">We use diverse RNA-seq protocols to update the annotation of rhizobial genomes with the inclusion of <em>tran<\/em>s-acting sRNAs, antisense sRNAs (asRNAs) and untranslated regions (5\u2019\/3\u2019-UTRs) of mRNAs. These new genome annotations are used as a reference to identify differentially expressed sRNAs in symbiotically relevant conditions by classical RNA-seq protocols.<\/p>\n[\/vc_column_text][image_with_animation image_url=\u00bb6694&#8243; animation=\u00bbFade In\u00bb hover_animation=\u00bbnone\u00bb constrain_group_1=\u00bbyes\u00bb alignment=\u00bbcenter\u00bb border_radius=\u00bbnone\u00bb box_shadow=\u00bbnone\u00bb image_loading=\u00bbdefault\u00bb max_width=\u00bb75%\u00bb max_width_mobile=\u00bbdefault\u00bb margin_top=\u00bb-15&#8243; margin_bottom=\u00bb-15&#8243;][vc_column_text]\n<h6 style=\"text-align: center;\"><strong>The complexity of the prokaryotic transcriptome as revealed by strand-specific RNA-seq. <\/strong>Categories of RNA species according to the location of their coding loci with respect to the annotated protein-coding genes. Number of sRNAs of each class expressed by S. meliloti are indicated. Most sRNAs are uncharacterized regulators of gene expression.<\/h6>\n[\/vc_column_text][\/vc_column_inner][\/vc_row_inner][vc_row_inner equal_height=\u00bbyes\u00bb content_placement=\u00bbmiddle\u00bb column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb text_align=\u00bbleft\u00bb][vc_column_inner column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bbdefault\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb][vc_column_text]\n<p style=\"text-align: justify;\"><strong>2. Riboregulation of rhizobial metabolism.<\/strong><\/p>\n<p style=\"text-align: justify;\">We are currently investigating in detail the function and activity mechanisms of three sRNAs called AbcR1, AbcR1 and NfeR1 that pervasively regulate mRNAs devoted to nutrient uptake and metabolism in the alfalfa symbiont <em>Sinorhizobium meliloti<\/em>. These sRNAs belong to the most studied class of riboregulators in bacteria, the so-called <em>trans<\/em>-sRNAs, which typically regulate translation and stability of multiple mRNAs by protein-assisted short and discontinuous base-pairing at the 5\u2019-region of the target transcripts.<\/p>\n[\/vc_column_text][image_with_animation image_url=\u00bb6695&#8243; animation=\u00bbFade In\u00bb hover_animation=\u00bbnone\u00bb alignment=\u00bbcenter\u00bb border_radius=\u00bbnone\u00bb box_shadow=\u00bbnone\u00bb image_loading=\u00bbdefault\u00bb max_width=\u00bb75%\u00bb max_width_mobile=\u00bbdefault\u00bb][vc_column_text]\n<h6 style=\"text-align: center;\"><strong>Activity mechanism of the bacterial <em>trans<\/em>-sRNAs. <\/strong>These sRNAs are differentially transcribed from independent promoters within intergenic regions in response to specific external signals and base-pair to the translation initiation region of multiple <em>trans<\/em>-encoded target mRNAs. These antisense interactions are usually assisted by and RNA chaperone such as Hfq, which acts as matchmaker. sRNA-mRNA interaction results in blocking of translation and\/or promotes mRNA degradation by RNases (e.g. YbeY and RNaseIII).<\/h6>\n[\/vc_column_text][\/vc_column_inner][\/vc_row_inner][vc_row_inner equal_height=\u00bbyes\u00bb content_placement=\u00bbmiddle\u00bb column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb text_align=\u00bbleft\u00bb][vc_column_inner column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bbdefault\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb][vc_column_text]\n<p style=\"text-align: justify;\"><strong>3. Regulation of symbiotic genes by antisense transcription.<\/strong><\/p>\n<p style=\"text-align: justify;\">Transcription from the antisense strand of protein-coding genes is pervasive in <em>S. meliloti<\/em>, being particularly abundant in genuine symbiotic regions of the pSymA megaplasmid. We study how asRNAs affect expression of nodulation and nitrogen-fixation genes in <em>S. meliloti<\/em>.<\/p>\n[\/vc_column_text][image_with_animation image_url=\u00bb6726&#8243; animation=\u00bbFade In\u00bb hover_animation=\u00bbnone\u00bb constrain_group_1=\u00bbyes\u00bb alignment=\u00bbcenter\u00bb border_radius=\u00bbnone\u00bb box_shadow=\u00bbnone\u00bb image_loading=\u00bbdefault\u00bb max_width=\u00bb75%\u00bb max_width_mobile=\u00bbdefault\u00bb margin_top=\u00bb25&#8243; margin_bottom=\u00bb25&#8243;][vc_column_text]\n<h6 style=\"text-align: center;\"><strong>Antisense transcription of the <em>S. meliloti<\/em> <em>fixN3<\/em> gene.<\/strong><\/h6>\n[\/vc_column_text][\/vc_column_inner][\/vc_row_inner][vc_row_inner equal_height=\u00bbyes\u00bb content_placement=\u00bbmiddle\u00bb column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb text_align=\u00bbleft\u00bb][vc_column_inner column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bbdefault\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb][vc_column_text]<strong>4. RNA-binding proteins and ribonucleases.<\/strong><\/p>\n<p style=\"text-align: justify;\">Using <em>S. meliloti<\/em> as model experimental system we investigate the function in riboregulation of the widespread bacterial chaperone Hfq and the endoribonucleases YbeY and RNase III. YbeY is a remarkable RNase identified in our laboratory that has an unprecedented ability among bacterial endoribonucleases to cleave both single- and double-stranded RNA substrates. We are also interested in the identification of novel RNA chaperones and the characterization of the whole set of ribonucleases in this bacterium.<\/p>\n[\/vc_column_text][image_with_animation image_url=\u00bb6697&#8243; animation=\u00bbFade In\u00bb hover_animation=\u00bbnone\u00bb alignment=\u00bbcenter\u00bb border_radius=\u00bbnone\u00bb box_shadow=\u00bbnone\u00bb image_loading=\u00bbdefault\u00bb max_width=\u00bb75%\u00bb max_width_mobile=\u00bbdefault\u00bb][vc_column_text]\n<h6 style=\"text-align: center;\"><strong>The <em>S. meliloti<\/em> Hfq protein.<\/strong> Genomic region, amino acid sequence and predicted structure.<\/h6>\n[\/vc_column_text][\/vc_column_inner][\/vc_row_inner][\/vc_column][\/vc_row][vc_row type=\u00bbfull_width_background\u00bb full_screen_row_position=\u00bbmiddle\u00bb column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb bg_color=\u00bb#ffffff\u00bb scene_position=\u00bbcenter\u00bb top_padding=\u00bb20&#8243; constrain_group_1=\u00bbyes\u00bb bottom_padding=\u00bb20&#8243; text_color=\u00bbdark\u00bb text_align=\u00bbleft\u00bb row_border_radius=\u00bbnone\u00bb row_border_radius_applies=\u00bbbg\u00bb id=\u00bbmethodological\u00bb overlay_strength=\u00bb0.3&#8243; gradient_direction=\u00bbleft_to_right\u00bb shape_divider_position=\u00bbbottom\u00bb bg_image_animation=\u00bbnone\u00bb shape_type=\u00bb\u00bb][vc_column column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb top_margin=\u00bb6&#8243; constrain_group_1=\u00bbyes\u00bb bottom_margin=\u00bb6&#8243; column_element_spacing=\u00bbdefault\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb tablet_text_alignment=\u00bbdefault\u00bb phone_text_alignment=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb][vc_column_text]\n<h3 style=\"text-align: center;\"><span style=\"color: #3e8932;\">Methodological approaches<\/span><\/h3>\n[\/vc_column_text][divider line_type=\u00bbSmall Line\u00bb line_alignment=\u00bbcenter\u00bb line_thickness=\u00bb1&#8243; divider_color=\u00bbaccent-color\u00bb animate=\u00bbyes\u00bb][vc_column_text]\n<ul>\n<li>Accurate identification of 5\u2019 and 3\u2019 boundaries of all cellular transcripts and primary characterization of the rhizobial transcriptomes: cutting-edge RNA-seq protocols (dRNA-seq, Cappable-seq, tagRNA-seq, or Term-seq).<\/li>\n<li>Functional characterization of sRNAs: molecular genetics, biochemistry, microbial\/plant physiology, microscopy, bioinformatics and genomics.<\/li>\n<li>Genome-wide identification of RNA-RNA, protein-RNA and protein-DNA interactions: methods based on high-throughput sequencing such as MAPS (MS2-affinity purification coupled with RNA sequencing), CLASH-seq (UV-Crosslinking, Ligation And Sequencing of RNA-RNA Hybrids), or ChIP-seq (chromatin immunoprecipitation).<\/li>\n<li>Catalytic versatility of the YbeY RNase: <em>in vitro<\/em> assays, crystallography, and structural biology.<\/li>\n<\/ul>\n[\/vc_column_text][divider line_type=\u00bbNo Line\u00bb custom_height=\u00bb15&#8243;][carousel script=\u00bbflickity\u00bb flickity_formatting=\u00bbdefault\u00bb desktop_cols_flickity=\u00bb1&#8243; desktop_small_cols_flickity=\u00bb1&#8243; tablet_cols_flickity=\u00bb1&#8243; flickity_controls=\u00bbnext_prev_arrows_overlaid\u00bb color=\u00bbdefault\u00bb flickity_overflow=\u00bbhidden\u00bb flickity_wrap_around=\u00bbwrap\u00bb flickity_spacing=\u00bbdefault\u00bb flickity_centered_cells=\u00bbtrue\u00bb column_padding=\u00bb0&#8243; flickity_element_spacing=\u00bbdefault\u00bb flickity_adaptive_height=\u00bbtrue\u00bb border_radius=\u00bbnone\u00bb][item simple_slider_bg_image_position=\u00bbdefault\u00bb simple_slider_overlay_strength=\u00bb0.3&#8243; id=\u00bb1639398353160-1&#8243; tab_id=\u00bb1639398353161-0&#8243; title=\u00bbElemento\u00bb][image_with_animation image_url=\u00bb6721&#8243; animation=\u00bbFade In\u00bb hover_animation=\u00bbnone\u00bb alignment=\u00bbcenter\u00bb border_radius=\u00bbnone\u00bb box_shadow=\u00bbnone\u00bb image_loading=\u00bbdefault\u00bb max_width=\u00bb75%\u00bb max_width_mobile=\u00bbdefault\u00bb][vc_column_text]\n<h6 style=\"text-align: center;\"><strong>Affinity chromatography-based determination of the sRNA interactomes. <\/strong>Shown is the setup of an assay involving AbcR2. The sRNA is tagged at its 5\u2019-end with the MS2 aptamer, thus allowing specific capture of the chimeric transcript along with its interacting protein and mRNA partners by an MS2-MBP (Maltose Binding Protein) fusion protein immobilized on an amylose resin. Lysates from bacteria expressing MS2-AbcR2 from an IPTG-inducible promoter in an Hfq-FLAG background are subjected to this affinity chromatography. AbcR2 is an Hfq-binding sRNA and therefore, chromatography can be monitored by Western blot probing of the different fractions with antiFLAG monoclonal antibodies. Proteins and RNA species bound to MS2-AbcR2 are profiled by mass spectrometry and RNA-seq, respectively.<\/h6>\n[\/vc_column_text][\/item][item simple_slider_bg_image_position=\u00bbdefault\u00bb simple_slider_overlay_strength=\u00bb0.3&#8243; title=\u00bbElemento\u00bb id=\u00bb1639398353211-7&#8243; tab_id=\u00bb1639398353211-8&#8243;][image_with_animation image_url=\u00bb6720&#8243; animation=\u00bbFade In\u00bb hover_animation=\u00bbnone\u00bb alignment=\u00bbcenter\u00bb border_radius=\u00bbnone\u00bb box_shadow=\u00bbnone\u00bb image_loading=\u00bbdefault\u00bb max_width=\u00bb50%\u00bb max_width_mobile=\u00bbdefault\u00bb][vc_column_text]\n<h6 style=\"text-align: center;\"><strong>A two-plasmid genetic reporter assay to delineate antisense sRNA-mRNA interactions <em>in vivo<\/em>. <\/strong>The figure shows the validation of the <em>prbA<\/em> mRNA as target of AbcR2. A <em>S. meliloti<\/em> AbcR1\/2 double deletion mutant is transformed with two compatible plasmids. One of the plasmids expresses AbcR2 from a constitutive (pSRK-R2) or IPTG-inducible (pSRK*-R2) promoter, the other expresses a translational fusion of <em>prbA<\/em> to the <em>egfp<\/em> reporter constitutively (pR<em>prbA::egfp<\/em>). Impact of AbcR2 on <em>prbA<\/em> translation is assessed by fluorescence measurements of the reporter strains.<\/h6>\n[\/vc_column_text][\/item][\/carousel][vc_row_inner column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb text_align=\u00bbleft\u00bb][vc_column_inner column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bbdefault\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb bg_image_animation=\u00bbnone\u00bb border_type=\u00bbsimple\u00bb column_border_width=\u00bbnone\u00bb column_border_style=\u00bbsolid\u00bb][\/vc_column_inner][\/vc_row_inner][\/vc_column][\/vc_row]\n","protected":false},"excerpt":{"rendered":"<p>[vc_row type=\u00bbin_container\u00bb full_screen_row_position=\u00bbmiddle\u00bb column_margin=\u00bbdefault\u00bb column_direction=\u00bbdefault\u00bb column_direction_tablet=\u00bbdefault\u00bb column_direction_phone=\u00bbdefault\u00bb scene_position=\u00bbcenter\u00bb text_color=\u00bbdark\u00bb text_align=\u00bbleft\u00bb row_border_radius=\u00bbnone\u00bb row_border_radius_applies=\u00bbbg\u00bb overlay_strength=\u00bb0.3&#8243; gradient_direction=\u00bbleft_to_right\u00bb shape_divider_position=\u00bbbottom\u00bb bg_image_animation=\u00bbnone\u00bb][vc_column column_padding=\u00bbno-extra-padding\u00bb column_padding_tablet=\u00bbinherit\u00bb column_padding_phone=\u00bbinherit\u00bb column_padding_position=\u00bball\u00bb column_element_spacing=\u00bbdefault\u00bb background_color_opacity=\u00bb1&#8243; background_hover_color_opacity=\u00bb1&#8243; column_shadow=\u00bbnone\u00bb column_border_radius=\u00bbnone\u00bb column_link_target=\u00bb_self\u00bb gradient_direction=\u00bbleft_to_right\u00bb overlay_strength=\u00bb0.3&#8243; width=\u00bb1\/1&#8243; tablet_width_inherit=\u00bbdefault\u00bb&#8230;<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-6637","page","type-page","status-publish"],"_links":{"self":[{"href":"https:\/\/grupos.eez.csic.es\/rhizorna\/wp-json\/wp\/v2\/pages\/6637","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/grupos.eez.csic.es\/rhizorna\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/grupos.eez.csic.es\/rhizorna\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/grupos.eez.csic.es\/rhizorna\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/grupos.eez.csic.es\/rhizorna\/wp-json\/wp\/v2\/comments?post=6637"}],"version-history":[{"count":18,"href":"https:\/\/grupos.eez.csic.es\/rhizorna\/wp-json\/wp\/v2\/pages\/6637\/revisions"}],"predecessor-version":[{"id":6693,"href":"https:\/\/grupos.eez.csic.es\/rhizorna\/wp-json\/wp\/v2\/pages\/6637\/revisions\/6693"}],"wp:attachment":[{"href":"https:\/\/grupos.eez.csic.es\/rhizorna\/wp-json\/wp\/v2\/media?parent=6637"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}