scholarly journals Signal Peptide-Dependent Protein Transport inBacillus subtilis: a Genome-Based Survey of the Secretome

2000 ◽  
Vol 64 (3) ◽  
pp. 515-547 ◽  
Author(s):  
Harold Tjalsma ◽  
Albert Bolhuis ◽  
Jan D. H. Jongbloed ◽  
Sierd Bron ◽  
Jan Maarten van Dijl
Keyword(s):  
Protein Secretion ◽  
Molecular Mechanisms ◽  
Protein Transport ◽  
Transport Systems ◽  
Future Research ◽  
Yeast Saccharomyces Cerevisiae ◽  
Transport Pathways ◽  
Amino Terminal ◽  
Cell Factories ◽  
A Genome

SUMMARY One of the most salient features of Bacillus subtilis and related bacilli is their natural capacity to secrete a variety of proteins into their environment, frequently to high concentrations. This has led to the commercial exploitation of bacilli as major “cell factories” for secreted enzymes. The recent sequencing of the genome of B. subtilis has provided major new impulse for analysis of the molecular mechanisms underlying protein secretion by this organism. Most importantly, the genome sequence has allowed predictions about the composition of the secretome, which includes both the pathways for protein transport and the secreted proteins. The present survey of the secretome describes four distinct pathways for protein export from the cytoplasm and approximately 300 proteins with the potential to be exported. By far the largest number of exported proteins are predicted to follow the major “Sec” pathway for protein secretion. In contrast, the twin-arginine translocation “Tat” pathway, a type IV prepilin-like export pathway for competence development, and ATP-binding cassette transporters can be regarded as “special-purpose” pathways, through which only a few proteins are transported. The properties of distinct classes of amino-terminal signal peptides, directing proteins into the various protein transport pathways, as well as the major components of each pathway are discussed. The predictions and comparisons in this review pinpoint important differences as well as similarities between protein transport systems in B. subtilis and other well-studied organisms, such as Escherichia coli and the yeast Saccharomyces cerevisiae. Thus, they may serve as a lead for future research and applications.

Membrane traffic related to endosome dynamics and protein secretion in filamentous fungi

2021 ◽  
Author(s):  
Yujiro Higuchi
Keyword(s):  
Filamentous Fungi ◽  
Protein Secretion ◽  
Secretory Pathway ◽  
Molecular Mechanisms ◽  
Membrane Traffic ◽  
Early Endosome ◽  
Protein Glycosylation ◽  
Hyphal Cell ◽  
Cell Factories ◽  
Membrane Contacts

ABSTRACT In eukaryotic cells, membrane-surrounded organelles are orchestrally organized spatiotemporally under environmental situations. Among such organelles, vesicular transports and membrane contacts occur to communicate each other, so-called membrane traffic. Filamentous fungal cells are highly polarized and thus membrane traffic is developed to have versatile functions. Early endosome (EE) is an endocytic organelle that dynamically exhibits constant long-range motility through the hyphal cell, which is proven to have physiological roles, such as other organelle distribution and signal transduction. Since filamentous fungal cells are also considered as cell factories, to produce valuable proteins extracellularly, molecular mechanisms of secretory pathway including protein glycosylation have been well investigated. In this review, molecular and physiological aspects of membrane traffic especially related to EE dynamics and protein secretion in filamentous fungi are summarized, and perspectives for application are also described.

scholarly journals Early transport: Protein secretion pathways in Archaea

2004 ◽  
Vol 26 (3) ◽  
pp. 16-18
Author(s):  
Albert Bolhuis
Keyword(s):  
Protein Secretion ◽  
Protein Transport ◽  
Transport Protein ◽  
Genomic Sequences ◽  
Transport Pathways ◽  
The Third ◽  
Main Protein ◽  
Secretion Pathways

The transport of proteins across membranes has been characterized in detail in Bacteria and Eukarya. Very little, however, is known about this process in the third domain of life, the Archaea. In recent years a number of groups have started to explore this area of research, but at present most information is derived from genomic sequences. Here, two of the main protein transport pathways found in archaea are briefly discussed and compared to bacterial and eukaryal systems.

Protein Transport Pathways in Bacillus subtilis: a Genome-Based Road Map

2014 ◽  
pp. 337-355 ◽  
Author(s):  
Jan Maarten Van Dijl ◽  
Albert Bolhuis ◽  
Harold Tjalsma ◽  
Jan D. H. Jongbloed ◽  
Anne De Jong ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Protein Transport ◽  
Transport Pathways ◽  
Road Map ◽  
A Genome

scholarly journals Vacuole Biogenesis in Saccharomyces cerevisiae: Protein Transport Pathways to the Yeast Vacuole

1998 ◽  
Vol 62 (1) ◽  
pp. 230-247 ◽  
Author(s):  
Nia J. Bryant ◽  
Tom H. Stevens
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Delivery ◽  
Secretory Pathway ◽  
Protein Transport ◽  
Transport Pathway ◽  
Yeast Saccharomyces Cerevisiae ◽  
Transport Pathways ◽  
Yeast Vacuole ◽  
Lysosome Biogenesis ◽  
Vacuolar Protein

SUMMARY Delivery of proteins to the vacuole of the yeast Saccharomyces cerevisiae provides an excellent model system in which to study vacuole and lysosome biogenesis and membrane traffic. This organelle receives proteins from a number of different routes, including proteins sorted away from the secretory pathway at the Golgi apparatus and endocytic traffic arising from the plasma membrane. Genetic analysis has revealed at least 60 genes involved in vacuolar protein sorting, numerous components of a novel cytoplasm-to-vacuole transport pathway, and a large number of proteins required for autophagy. Cell biological and biochemical studies have provided important molecular insights into the various protein delivery pathways to the yeast vacuole. This review describes the various pathways to the vacuole and illustrates how they are related to one another in the vacuolar network of S. cerevisiae.

scholarly journals Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance

2011 ◽  
Vol 43 (14) ◽  
pp. 855-872 ◽  
Author(s):  
Ajit N. Shah ◽  
Daniela Cadinu ◽  
R. Michael Henke ◽  
Xiantong Xin ◽  
Ranita Ghosh Dastidar ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
Molecular Mechanisms ◽  
Specific Protein ◽  
Hypoxia Tolerance ◽  
Deletion Mutants ◽  
Yeast Saccharomyces Cerevisiae ◽  
Genome Wide ◽  
A Genome ◽  
In The Wild ◽  
Induced Changes

Hypoxia is a widely occurring condition experienced by diverse organisms under numerous physiological and disease conditions. To probe the molecular mechanisms underlying hypoxia responses and tolerance, we performed a genome-wide screen to identify mutants with enhanced hypoxia tolerance in the model eukaryote, the yeast Saccharomyces cerevisiae . Yeast provides an excellent model for genomic and proteomic studies of hypoxia. We identified five genes whose deletion significantly enhanced hypoxia tolerance. They are RAI1, NSR1, BUD21, RPL20A, and RSM22, all of which encode functions involved in ribosome biogenesis. Further analysis of the deletion mutants showed that they minimized hypoxia-induced changes in polyribosome profiles and protein synthesis. Strikingly, proteomic analysis by using the iTRAQ profiling technology showed that a substantially fewer number of proteins were changed in response to hypoxia in the deletion mutants, compared with the parent strain. Computational analysis of the iTRAQ data indicated that the activities of a group of regulators were regulated by hypoxia in the wild-type parent cells, but such regulation appeared to be diminished in the deletion strains. These results show that the deletion of one of the genes involved in ribosome biogenesis leads to the reversal of hypoxia-induced changes in gene expression and related regulators. They suggest that modifying ribosomal function is an effective mechanism to minimize hypoxia-induced specific protein changes and to confer hypoxia tolerance. These results may have broad implications in understanding hypoxia responses and tolerance in diverse eukaryotes ranging from yeast to humans.

scholarly journals Moderate Expression of SEC16 Increases Protein Secretion by Saccharomyces cerevisiae

2017 ◽  
Vol 83 (14) ◽  
Author(s):  
Jichen Bao ◽  
Mingtao Huang ◽  
Dina Petranovic ◽  
Jens Nielsen
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Endoplasmic Reticulum ◽  
Protein Secretion ◽  
Recombinant Proteins ◽  
Secretory Pathway ◽  
Cell Factory ◽  
Amylase Secretion ◽  
Content Type ◽  
Cell Factories ◽  
A Genome

ABSTRACT The yeast Saccharomyces cerevisiae is widely used to produce biopharmaceutical proteins. However, the limited capacity of the secretory pathway may reduce its productivity. Here, we increased the secretion of a heterologous α-amylase, a model protein used for studying the protein secretory pathway in yeast, by moderately overexpressing SEC16, which is involved in protein translocation from the endoplasmic reticulum to the Golgi apparatus. The moderate overexpression of SEC16 increased α-amylase secretion by generating more endoplasmic reticulum exit sites. The production of reactive oxygen species resulting from the heterologous α-amylase production was reduced. A genome-wide expression analysis indicated decreased endoplasmic reticulum stress in the strain that moderately overexpressed SEC16, which was consistent with a decreased volume of the endoplasmic reticulum. Additionally, fewer mitochondria were observed. Finally, the moderate overexpression of SEC16 was shown to improve the secretion of two other recombinant proteins, Trichoderma reesei endoglucanase I and Rhizopus oryzae glucan-1,4-α-glucosidase, indicating that this mechanism is of general relevance. IMPORTANCE There is an increasing demand for recombinant proteins to be used as enzymes and pharmaceuticals. The yeast Saccharomyces cerevisiae is a cell factory that is widely used to produce recombinant proteins. Our study revealed that moderate overexpression of SEC16 increased recombinant protein secretion in S. cerevisiae. This new strategy can be combined with other targets to engineer cell factories to efficiently produce protein in the future.

scholarly journals Genome-wide Analysis of AP-3–dependent Protein Transport in Yeast

2009 ◽  
Vol 20 (5) ◽  
pp. 1592-1604 ◽  
Author(s):  
Vikram C. Anand ◽  
Lydia Daboussi ◽  
Todd C. Lorenz ◽  
Gregory S. Payne
Keyword(s):  
Protein Transport ◽  
Adaptor Protein ◽  
Subcellular Fractionation ◽  
Type I ◽  
Transport Pathways ◽  
Genome Wide ◽  
A Genome ◽  
Rapid Generation ◽  
Vacuolar Protein ◽  
Er Export

The evolutionarily conserved adaptor protein-3 (AP-3) complex mediates cargo-selective transport to lysosomes and lysosome-related organelles. To identify proteins that function in AP-3–mediated transport, we performed a genome-wide screen in Saccharomyces cerevisiae for defects in the vacuolar maturation of alkaline phosphatase (ALP), a cargo of the AP-3 pathway. Forty-nine gene deletion strains were identified that accumulated precursor ALP, many with established defects in vacuolar protein transport. Maturation of a vacuolar membrane protein delivered via a separate, clathrin-dependent pathway, was affected in all strains except those with deletions of YCK3, encoding a vacuolar type I casein kinase; SVP26, encoding an endoplasmic reticulum (ER) export receptor for ALP; and AP-3 subunit genes. Subcellular fractionation and fluorescence microscopy revealed ALP transport defects in yck3Δ cells. Characterization of svp26Δ cells revealed a role for Svp26p in ER export of only a subset of type II membrane proteins. Finally, ALP maturation kinetics in vac8Δ and vac17Δ cells suggests that vacuole inheritance is important for rapid generation of proteolytically active vacuolar compartments in daughter cells. We propose that the cargo-selective nature of the AP-3 pathway in yeast is achieved by AP-3 and Yck3p functioning in concert with machinery shared by other vacuolar transport pathways.

Bi-directional trafficking between the trans-Golgi network and the endosomal/lysosomal system

2000 ◽  
Vol 113 (12) ◽  
pp. 2093-2101 ◽  
Author(s):  
W.M. Rohn ◽  
Y. Rouille ◽  
S. Waguri ◽  
B. Hoflack
Keyword(s):  
Molecular Mechanisms ◽  
Protein Transport ◽  
Transport Systems ◽  
Membrane Glycoproteins ◽  
Trans Golgi Network ◽  
Sorting Signals ◽  
Lysosomal System ◽  
Golgi Network ◽  
Endosomal System ◽  
Assembly Proteins

Protein transport in the secretory and endocytic pathways of eukaryotic cells is mediated by vesicular transport intermediates. Their formation is a tightly controlled multistep process in which coat components are recruited onto specific membranes, and cargo, as well as targeting molecules, become segregated into nascent vesicles. At the trans-Golgi network, two transport systems deliver cargo molecules to the endosomal system. They can be distinguished with regard to coat components that select cargo molecules. AP-1 assembly proteins mediate transport of MPRs and furin, whereas AP-3 adaptors mediate transport of lysosomal membrane glycoproteins to the endosomal/lysosomal system. The molecular basis for protein-specific sorting lies within sorting signals that are present in the cytoplasmic tails of cargo proteins and allow specific interactions with individual coat components. In order to maintain cellular homeostasis, some proteins are retrieved from endosomal compartments and transported back to the trans-Golgi network. Distinct points for protein retrieval exist within the endosomal system, retrieval occurring from either early or late endosomes. Whereas significant progress has been made in recent years in identifying anterograde and retrograde transport pathways, the molecular mechanisms underlying protein sorting and retrieval are only poorly defined. Recently, however, novel vesicle coats (e.g. AP-4) and proteins that might be involved in sorting (e.g. PACS-1 and TIP47) have been described, and the interactions between assembly proteins and sorting signals are becoming increasingly well defined.

Cancer Proteomics: New Horizons and Insights into Therapeutic Applications

2020 ◽  
Vol 17 ◽  
Author(s):  
Perumal Subramaniana ◽  
Jaime Jacqueline Jayapalan ◽  
Puteri Shafinaz Abdul-Rahmanb
Keyword(s):  
Molecular Mechanisms ◽  
Rapid Development ◽  
New Horizons ◽  
Cancer Management ◽  
Proteomic Approach ◽  
Cancer Proteomics ◽  
Therapeutic Outcomes ◽  
A Genome ◽  
Highly Sensitive ◽  
Dimensional Electrophoresis

A proteome is an efficient rendition of a genome, unswervingly controlling various cancer processes. Molecular mechanisms of several cancer processes have been unraveled by proteomic approach. Thus far, numerous tumors of diverse status have been investigated by two-dimensional electrophoresis. Numerous biomarkers have been recognized and precise categorization of apparent lesions has led to the timely detection of various cancers in persons at peril. Currently used pioneering approaches and technologies in proteomics have led to highly sensitive assays of cancer biomarkers and improved the early diagnosis of various cancers. The discovery of novel and definite biomarker signatures further widened our perceptive of the disease and novel potent drugs for efficient and aimed therapeutic outcomes in persistent cancers have emerged. However, a major limitation, even today, of proteomics is resolving and quantifying the proteins of low abundance. Despite the rapid development of proteomic technologies and their applications in cancer management, annulling the shortcomings of present proteomic technologies and development of better methods are still desirable. The main objectives of this review are to discuss the developing aspects, merits and demerits of pharmacoproteomics, redox proteomics, novel approaches and therapies being used for various types of cancer based on proteome studies.

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