Atypical Carboxysome Loci: JEEPs or Junk?
Atypical Carboxysome Loci: JEEPs or Junk?
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DOI：
10.3389/fmicb.2022.872708
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发表时间：
2022
影响因子：
5.2
通讯作者：
中科院分区：
文献类型：
--
作者：
负责地球上相当大一部分CO2固定的羧基体是蛋白质微区室，存在于域细菌的许多自养成员中，主要来自变形菌门和蓝细菌门。羧基体通过Calvin-Benson-Bassham（CBB）循环促进CO2固定，特别是在CO2浓度可变或较低或O2丰富的条件下。这些微区室由二十面体壳组成，所述二十面体壳含有酶核酮糖1，5-羧化酶/加氧酶（RubisCO）和碳酸酐酶。它们作为CO2浓缩机制的一部分发挥作用，细胞通过主动转运在细胞质中积累HCO 3 −，HCO 3 −通过羧基体壳蛋白的孔进入羧基体，羧基体碳酸酐酶促进HCO 3 −转化为CO2，RubisCO将其固定。已描述了两种形式的羧基体：α-羧基体和β-羧基体，它们独立于祖先微区室产生。变形菌和一些蓝细菌中存在的α-羧基体具有由四种类型的蛋白质[CsoS 1六聚体、CsoS 4五聚体、CsoS 2组装蛋白和α-羧基体碳酸酐酶（CsoSCA）]组成的外壳，并含有IA型RubisCO（CbbL和CbbS）。在大多数情况下，这些组分在基因座中彼此靠近地编码在基因组中，并且作为操纵子一起转录。有趣的是，基因组测序揭示了一些α-羧基体基因座缺失编码一种或多种这些组分的基因。一些基因座缺少编码RubisCO的基因，另一些基因座缺少编码碳酸酐酶的基因，一些基因座缺少壳蛋白基因，并且在一些生物体中，与编码羧基体相关碳酸酐酶的基因同源的基因是基因组中存在的唯一羧基体相关基因。考虑到RubisCO、组装因子、碳酸酐酶和壳蛋白都是羧基体功能所必需的，这些缺失是相当有趣的。在这篇综述中，我们提供了一个概述的最新研究的结构组成部分的carboxysomes，描述的基因组背景和分类学分布的非典型carboxysomes位点，并提出这些变体的功能。我们认为，这些非典型位点是JEEPs，它具有基于Just Enough Essential Parts存在的修改功能。
Carboxysomes, responsible for a substantial fraction of CO2 fixation on Earth, are proteinaceous microcompartments found in many autotrophic members of domain Bacteria, primarily from the phyla Proteobacteria and Cyanobacteria. Carboxysomes facilitate CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle, particularly under conditions where the CO2 concentration is variable or low, or O2 is abundant. These microcompartments are composed of an icosahedral shell containing the enzymes ribulose 1,5-carboxylase/oxygenase (RubisCO) and carbonic anhydrase. They function as part of a CO2 concentrating mechanism, in which cells accumulate HCO3− in the cytoplasm via active transport, HCO3− enters the carboxysomes through pores in the carboxysomal shell proteins, and carboxysomal carbonic anhydrase facilitates the conversion of HCO3− to CO2, which RubisCO fixes. Two forms of carboxysomes have been described: α-carboxysomes and β-carboxysomes, which arose independently from ancestral microcompartments. The α-carboxysomes present in Proteobacteria and some Cyanobacteria have shells comprised of four types of proteins [CsoS1 hexamers, CsoS4 pentamers, CsoS2 assembly proteins, and α-carboxysomal carbonic anhydrase (CsoSCA)], and contain form IA RubisCO (CbbL and CbbS). In the majority of cases, these components are encoded in the genome near each other in a gene locus, and transcribed together as an operon. Interestingly, genome sequencing has revealed some α-carboxysome loci that are missing genes encoding one or more of these components. Some loci lack the genes encoding RubisCO, others lack a gene encoding carbonic anhydrase, some loci are missing shell protein genes, and in some organisms, genes homologous to those encoding the carboxysome-associated carbonic anhydrase are the only carboxysome-related genes present in the genome. Given that RubisCO, assembly factors, carbonic anhydrase, and shell proteins are all essential for carboxysome function, these absences are quite intriguing. In this review, we provide an overview of the most recent studies of the structural components of carboxysomes, describe the genomic context and taxonomic distribution of atypical carboxysome loci, and propose functions for these variants. We suggest that these atypical loci are JEEPs, which have modified functions based on the presence of Just Enough Essential Parts.
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DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
DOI：
10.3390/life5021141
发表时间：
2015-03-27
期刊：
Life (Basel, Switzerland)
影响因子：
--
作者：
Cai F;Dou Z;Bernstein SL;Leverenz R;Williams EB;Heinhorst S;Shively J;Cannon GC;Kerfeld CA
通讯作者：
Kerfeld CA
影响因子：
64.8
作者：
Jumper J;Evans R;Pritzel A;Green T;Figurnov M;Ronneberger O;Tunyasuvunakool K;Bates R;Žídek A;Potapenko A;Bridgland A;Meyer C;Kohl SAA;Ballard AJ;Cowie A;Romera-Paredes B;Nikolov S;Jain R;Adler J;Back T;Petersen S;Reiman D;Clancy E;Zielinski M;Steinegger M;Pacholska M;Berghammer T;Bodenstein S;Silver D;Vinyals O;Senior AW;Kavukcuoglu K;Kohli P;Hassabis D
通讯作者：
Hassabis D
影响因子：
14.9
作者：
Chen IA;Chu K;Palaniappan K;Pillay M;Ratner A;Huang J;Huntemann M;Varghese N;White JR;Seshadri R;Smirnova T;Kirton E;Jungbluth SP;Woyke T;Eloe-Fadrosh EA;Ivanova NN;Kyrpides NC
通讯作者：
Kyrpides NC
影响因子：
2.6
作者：
Cannon, GC;Baker, SH;Shively, JM
通讯作者：
Shively, JM