Atypical Carboxysome Loci: JEEPs or Junk?
Abstract
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 locimore »
- Authors:
-
- Michigan State Univ., East Lansing, MI (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. of South Florida, Tampa, FL (United States)
- Publication Date:
- Research Org.:
- Michigan State Univ., East Lansing, MI (United States). MSU-DOE Plant Research Laboratory; Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of South Florida, Tampa, FL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Contributing Org.:
- USF Genomics Class 2020; USF Genomics Class 2021
- OSTI Identifier:
- 1902065
- Alternate Identifier(s):
- OSTI ID: 1893867
- Grant/Contract Number:
- FG02-91ER20021; AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 13; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; carboxysome; microcompartment; carbonic anhydrase; carbon dioxide fixation; autotroph
Citation Formats
Sutter, Markus, Kerfeld, Cheryl A., and Scott, Kathleen M. Atypical Carboxysome Loci: JEEPs or Junk?. United States: N. p., 2022.
Web. doi:10.3389/fmicb.2022.872708.
Sutter, Markus, Kerfeld, Cheryl A., & Scott, Kathleen M. Atypical Carboxysome Loci: JEEPs or Junk?. United States. https://doi.org/10.3389/fmicb.2022.872708
Sutter, Markus, Kerfeld, Cheryl A., and Scott, Kathleen M. Fri .
"Atypical Carboxysome Loci: JEEPs or Junk?". United States. https://doi.org/10.3389/fmicb.2022.872708. https://www.osti.gov/servlets/purl/1902065.
@article{osti_1902065,
title = {Atypical Carboxysome Loci: JEEPs or Junk?},
author = {Sutter, Markus and Kerfeld, Cheryl A. and Scott, Kathleen M.},
abstractNote = {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.},
doi = {10.3389/fmicb.2022.872708},
journal = {Frontiers in Microbiology},
number = ,
volume = 13,
place = {United States},
year = {Fri May 20 00:00:00 EDT 2022},
month = {Fri May 20 00:00:00 EDT 2022}
}
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