1
|
Estrada K, Garciarrubio A, Merino E. Unraveling the plasticity of translation initiation in prokaryotes: Beyond the invariant Shine-Dalgarno sequence. PLoS One 2024; 19:e0289914. [PMID: 38206950 PMCID: PMC10783764 DOI: 10.1371/journal.pone.0289914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/28/2023] [Indexed: 01/13/2024] Open
Abstract
Translation initiation in prokaryotes is mainly defined, although not exclusively, by the interaction between the anti-Shine-Dalgarno sequence (antiSD), located at the 3'-terminus of the 16S ribosomal RNA, and a complementary sequence, the ribosome binding site, or Shine-Dalgarno (SD), located upstream of the start codon in prokaryotic mRNAs. The antiSD has a conserved 5'-CCUCC-3' core, but inter-species variations have been found regarding the participation of flanking bases in binding. These variations have been described for certain bacteria and, to a lesser extent, for some archaea. To further analyze these variations, we conducted binding-energy prediction analyses on over 6,400 genomic sequences from both domains. We identified 15 groups of antiSD variants that could be associated with the organisms' phylogenetic origin. Additionally, our findings revealed that certain organisms exhibit variations in the core itself. Importantly, an unaltered core is not necessarily required for the interaction between the 3'-terminus of the rRNA and the region preceding the AUG of the mRNA. In our study, we classified organisms into four distinct categories: i) those possessing a conserved core and demonstrating binding; ii) those with a conserved core but lacking evidence of binding; iii) those exhibiting binding in the absence of a conserved core; and iv) those lacking both a conserved core and evidence of binding. Our results demonstrate the flexibility of organisms in evolving different sequences involved in translation initiation beyond the traditional Shine-Dalgarno sequence. These findings are discussed in terms of the evolution of translation initiation in prokaryotic organisms.
Collapse
Affiliation(s)
- Karel Estrada
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, México
- Massive Sequencing and Bioinformatics Unit, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Alejandro Garciarrubio
- Department of Cell Engineering and Biocatalysis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Enrique Merino
- Department of Molecular Microbiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| |
Collapse
|
2
|
Baes R, Grünberger F, Pyr dit Ruys S, Couturier M, De Keulenaer S, Skevin S, Van Nieuwerburgh F, Vertommen D, Grohmann D, Ferreira-Cerca S, Peeters E. Transcriptional and translational dynamics underlying heat shock response in the thermophilic crenarchaeon Sulfolobus acidocaldarius. mBio 2023; 14:e0359322. [PMID: 37642423 PMCID: PMC10653856 DOI: 10.1128/mbio.03593-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 06/29/2023] [Indexed: 08/31/2023] Open
Abstract
IMPORTANCE Heat shock response is the ability to respond adequately to sudden temperature increases that could be harmful for cellular survival and fitness. It is crucial for microorganisms living in volcanic hot springs that are characterized by high temperatures and large temperature fluctuations. In this study, we investigated how S. acidocaldarius, which grows optimally at 75°C, responds to heat shock by altering its gene expression and protein production processes. We shed light on which cellular processes are affected by heat shock and propose a hypothesis on underlying regulatory mechanisms. This work is not only relevant for the organism's lifestyle, but also with regard to its evolutionary status. Indeed, S. acidocaldarius belongs to the archaea, an ancient group of microbes that is more closely related to eukaryotes than to bacteria. Our study thus also contributes to a better understanding of the early evolution of heat shock response.
Collapse
Affiliation(s)
- Rani Baes
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Felix Grünberger
- Institute of Microbiology and Archaea Centre, Universität Regensburg, Regensburg, Germany
| | | | - Mohea Couturier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sarah De Keulenaer
- NXTGNT, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Sonja Skevin
- NXTGNT, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | | | - Didier Vertommen
- Institut de Duve, Université Catholique de Louvain, Brussels, Belgium
| | - Dina Grohmann
- Institute of Microbiology and Archaea Centre, Universität Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Cellular Biochemistry of Microorganisms, Biochemie III, Universität Regensburg, Regensburg, Germany
- Laboratoire de Biologie Structurale de la Cellule (BIOC), UMR 7654 -CNRS, Ecole polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| |
Collapse
|
3
|
Guo XP, Yan HQ, Yang W, Yin Z, Vadyvaloo V, Zhou D, Sun YC. A frameshift in Yersinia pestis rcsD alters canonical Rcs signalling to preserve flea-mammal plague transmission cycles. eLife 2023; 12:e83946. [PMID: 37010269 PMCID: PMC10191623 DOI: 10.7554/elife.83946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/02/2023] [Indexed: 04/04/2023] Open
Abstract
Multiple genetic changes in the enteric pathogen Yersinia pseudotuberculosis have driven the emergence of Yesinia pestis, the arthropod-borne, etiological agent of plague. These include developing the capacity for biofilm-dependent blockage of the flea foregut to enable transmission by flea bite. Previously, we showed that pseudogenization of rcsA, encoding a component of the Rcs signalling pathway, is an important evolutionary step facilitating Y. pestis flea-borne transmission. Additionally, rcsD, another important gene in the Rcs system, harbours a frameshift mutation. Here, we demonstrated that this rcsD mutation resulted in production of a small protein composing the C-terminal RcsD histidine-phosphotransferase domain (designated RcsD-Hpt) and full-length RcsD. Genetic analysis revealed that the rcsD frameshift mutation followed the emergence of rcsA pseudogenization. It further altered the canonical Rcs phosphorylation signal cascade, fine-tuning biofilm production to be conducive with retention of the pgm locus in modern lineages of Y. pestis. Taken together, our findings suggest that a frameshift mutation in rcsD is an important evolutionary step that fine-tuned biofilm production to ensure perpetuation of flea-mammal plague transmission cycles.
Collapse
Affiliation(s)
- Xiao-Peng Guo
- NHC key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Hai-Qin Yan
- Department of Basic Medical Sciences, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical CollegeBengbuChina
- Paul G. Allen School for Global Health, Washington State UniversityPullmanUnited States
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Viveka Vadyvaloo
- Paul G. Allen School for Global Health, Washington State UniversityPullmanUnited States
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Yi-Cheng Sun
- NHC key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| |
Collapse
|
4
|
Kohl MP, Kompatscher M, Clementi N, Holl L, Erlacher M. Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli. Nucleic Acids Res 2022; 51:271-289. [PMID: 36546769 PMCID: PMC9841429 DOI: 10.1093/nar/gkac1175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/16/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
During initiation, the ribosome is tasked to efficiently recognize open reading frames (ORFs) for accurate and fast translation of mRNAs. A critical step is start codon recognition, which is modulated by initiation factors, mRNA structure, a Shine Dalgarno (SD) sequence and the start codon itself. Within the Escherichia coli genome, we identified more than 50 annotated initiation sites harboring AUGUG or GUGUG sequence motifs that provide two canonical start codons, AUG and GUG, in immediate proximity. As these sites may challenge start codon recognition, we studied if and how the ribosome is accurately guided to the designated ORF, with a special focus on the SD sequence as well as adenine at the fourth coding sequence position (A4). By in vitro and in vivo experiments, we characterized key requirements for unambiguous start codon recognition, but also discovered initiation sites that lead to the translation of both overlapping reading frames. Our findings corroborate the existence of an ambiguous translation initiation mechanism, implicating a multitude of so far unrecognized ORFs and translation products in bacteria.
Collapse
Affiliation(s)
- Maximilian P Kohl
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Maria Kompatscher
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Clementi
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lena Holl
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Matthias D Erlacher
- To whom correspondence should be addressed. Tel: +43 512900370256; Fax: +43 512900373100;
| |
Collapse
|
5
|
Bharmal MHM, Gega A, Schrader JM. A combination of mRNA features influence the efficiency of leaderless mRNA translation initiation. NAR Genom Bioinform 2021; 3:lqab081. [PMID: 34568822 PMCID: PMC8459731 DOI: 10.1093/nargab/lqab081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/03/2021] [Accepted: 08/27/2021] [Indexed: 12/30/2022] Open
Abstract
Bacterial translation is thought to initiate by base pairing of the 16S rRNA and the Shine-Dalgarno sequence in the mRNA's 5' untranslated region (UTR). However, transcriptomics has revealed that leaderless mRNAs, which completely lack any 5' UTR, are broadly distributed across bacteria and can initiate translation in the absence of the Shine-Dalgarno sequence. To investigate the mechanism of leaderless mRNA translation initiation, synthetic in vivo translation reporters were designed that systematically tested the effects of start codon accessibility, leader length, and start codon identity on leaderless mRNA translation initiation. Using these data, a simple computational model was built based on the combinatorial relationship of these mRNA features that can accurately classify leaderless mRNAs and predict the translation initiation efficiency of leaderless mRNAs. Thus, start codon accessibility, leader length, and start codon identity combine to define leaderless mRNA translation initiation in bacteria.
Collapse
Affiliation(s)
| | - Alisa Gega
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Jared M Schrader
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| |
Collapse
|
6
|
Start Codon Recognition in Eukaryotic and Archaeal Translation Initiation: A Common Structural Core. Int J Mol Sci 2019; 20:ijms20040939. [PMID: 30795538 PMCID: PMC6412873 DOI: 10.3390/ijms20040939] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 01/12/2023] Open
Abstract
Understanding molecular mechanisms of ribosomal translation sheds light on the emergence and evolution of protein synthesis in the three domains of life. Universally, ribosomal translation is described in three steps: initiation, elongation and termination. During initiation, a macromolecular complex assembled around the small ribosomal subunit selects the start codon on the mRNA and defines the open reading frame. In this review, we focus on the comparison of start codon selection mechanisms in eukaryotes and archaea. Eukaryotic translation initiation is a very complicated process, involving many initiation factors. The most widespread mechanism for the discovery of the start codon is the scanning of the mRNA by a pre-initiation complex until the first AUG codon in a correct context is found. In archaea, long-range scanning does not occur because of the presence of Shine-Dalgarno (SD) sequences or of short 5′ untranslated regions. However, archaeal and eukaryotic translation initiations have three initiation factors in common: e/aIF1, e/aIF1A and e/aIF2 are directly involved in the selection of the start codon. Therefore, the idea that these archaeal and eukaryotic factors fulfill similar functions within a common structural ribosomal core complex has emerged. A divergence between eukaryotic and archaeal factors allowed for the adaptation to the long-range scanning process versus the SD mediated prepositioning of the ribosome.
Collapse
|
7
|
Abstract
ABSTRACT
Previously, leaderless mRNAs (lmRNAs) were perceived to make up only a minor fraction of the transcriptome in bacteria. However, advancements in RNA sequencing technology are uncovering vast numbers of lmRNAs, particularly in archaea,
Actinobacteria
, and extremophiles and thus underline their significance in cellular physiology and regulation. Due to the absence of conventional ribosome binding signals, lmRNA translation initiation is distinct from canonical mRNAs and can therefore be differentially regulated. The ribosome’s inherent ability to bind a 5′-terminal AUG can stabilize and protect the lmRNA from degradation or allow ribosomal loading for downstream initiation events. As a result, lmRNAs remain translationally competent during a variety of physiological conditions, allowing them to contribute to multiple regulatory mechanisms. Furthermore, the abundance of lmRNAs can increase during adverse conditions through the upregulation of lmRNA transcription from alternative promoters or by the generation of lmRNAs from canonical mRNAs cleaved by an endonucleolytic toxin. In these ways, lmRNA translation can continue during stress and contribute to regulation, illustrating their importance in the cell. Due to their presence in all domains of life and their ability to be translated by heterologous hosts, lmRNAs appear further to represent ancestral transcripts that might allow us to study the evolution of the ribosome and the translational process.
Collapse
|
8
|
Nakagawa S, Niimura Y, Gojobori T. Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine-Dalgarno sequence in prokaryotes. Nucleic Acids Res 2017; 45:3922-3931. [PMID: 28334743 PMCID: PMC5397173 DOI: 10.1093/nar/gkx124] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/11/2017] [Indexed: 02/01/2023] Open
Abstract
In prokaryotes, translation initiation is believed to occur through an interaction between the 3΄ tail of a 16S rRNA and a corresponding Shine–Dalgarno (SD) sequence in the 5΄ untranslated region (UTR) of an mRNA. However, some genes lack SD sequences (non-SD genes), and the fraction of non-SD genes in a genome varies depending on the prokaryotic species. To elucidate non-SD translation initiation mechanisms in prokaryotes from an evolutionary perspective, we statistically examined the nucleotide frequencies around the initiation codons in non-SD genes from 260 prokaryotes (235 bacteria and 25 archaea). We identified distinct nucleotide frequency biases upstream of the initiation codon in bacteria and archaea, likely because of the presence of leaderless mRNAs lacking a 5΄ UTR. Moreover, we observed overall similarities in the nucleotide patterns between upstream and downstream regions of the initiation codon in all examined phyla. Symmetric nucleotide frequency biases might facilitate translation initiation by preventing the formation of secondary structures around the initiation codon. These features are more prominent in species’ genomes that harbor large fractions of non-SD sequences, suggesting that a reduced stability around the initiation codon is important for efficient translation initiation in prokaryotes.
Collapse
Affiliation(s)
- So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara 259-1193, Japan.,Micro/Nano Technology Center, Tokai University, Hiratsuka 259-1292, Japan
| | - Yoshihito Niimura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Takashi Gojobori
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal 23955-6900, Kingdom of Saudi Arabia
| |
Collapse
|
9
|
Critical reflections on synthetic gene design for recombinant protein expression. Curr Opin Struct Biol 2016; 38:155-62. [DOI: 10.1016/j.sbi.2016.07.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/29/2016] [Accepted: 07/06/2016] [Indexed: 11/17/2022]
|