scholarly journals Assembly of the algal CO2-fixing organelle, the pyrenoid, is guided by a Rubisco-binding motif

2020 ◽  
Vol 6 (46) ◽  
pp. eabd2408 ◽  
Author(s):  
Moritz T. Meyer ◽  
Alan K. Itakura ◽  
Weronika Patena ◽  
Lianyong Wang ◽  
Shan He ◽  
...  
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Binding Motif ◽  
Sequence Motif ◽  
Protein Motif ◽  
Target Proteins ◽  
Single Protein ◽  
The Matrix ◽  
Membrane Tubules ◽  
Necessary And Sufficient

Approximately one-third of the Earth’s photosynthetic CO2 assimilation occurs in a pyrenoid, an organelle containing the CO2-fixing enzyme Rubisco. How constituent proteins are recruited to the pyrenoid and how the organelle’s subcompartments—membrane tubules, a surrounding phase-separated Rubisco matrix, and a peripheral starch sheath—are held together is unknown. Using the model alga Chlamydomonas reinhardtii, we found that pyrenoid proteins share a sequence motif. We show that the motif is necessary and sufficient to target proteins to the pyrenoid and that the motif binds to Rubisco, suggesting a mechanism for targeting. The presence of the Rubisco-binding motif on proteins that localize to the tubules and on proteins that localize to the matrix–starch sheath interface suggests that the motif holds the pyrenoid’s three subcompartments together. Our findings advance our understanding of pyrenoid biogenesis and illustrate how a single protein motif can underlie the architecture of a complex multilayered phase-separated organelle.

scholarly journals Assembly of the algal CO2-fixing organelle, the pyrenoid, is guided by a Rubisco-binding motif

2020 ◽  
Author(s):  
Moritz T. Meyer ◽  
Alan K. Itakura ◽  
Weronika Patena ◽  
Lianyong Wang ◽  
Shan He ◽  
...  
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Binding Motif ◽  
Sequence Motif ◽  
Protein Motif ◽  
Target Proteins ◽  
Single Protein ◽  
The Matrix ◽  
Membrane Tubules

AbstractApproximately one-third of the Earth’s photosynthetic CO2 assimilation occurs in a pyrenoid, an organelle containing the CO2-fixing enzyme Rubisco. How constituent proteins are recruited to the pyrenoid, and how the organelle’s sub-compartments - membrane tubules, a surrounding phase-separated Rubisco matrix, and a peripheral starch sheath - are held together is unknown. Using the model alga Chlamydomonas reinhardtii, we discovered that pyrenoid proteins share a sequence motif. We show that the motif is sufficient to target proteins to the pyrenoid and that the motif binds to Rubisco, suggesting a mechanism for targeting. The presence of the Rubisco-binding motif on proteins that localize to the tubules and on proteins that localize to the matrix-starch sheath interface suggests that the motif holds the pyrenoid’s three sub-compartments together. Our findings advance our understanding of pyrenoid biogenesis and illustrate how a single protein motif can underlie the architecture of a complex multi-layered phase-separated organelle.One Sentence SummaryA ubiquitous Rubisco-binding motif targets proteins to the pyrenoid and holds together the pyrenoid’s three sub-compartments.

scholarly journals Complex-analytic and matrix-analytic solutions for a queueing system with group service controlled by arrivals

2000 ◽  
Vol 13 (4) ◽  
pp. 415-427
Author(s):  
Lev Abolnikov ◽  
Alexander Dukhovny
Keyword(s):  
Block Size ◽  
Iteration Process ◽  
Analytic Solutions ◽  
Analytic Method ◽  
Service Time Distribution ◽  
Matrix Analytic Method ◽  
Queueing Process ◽  
The Matrix ◽  
Matrix Iteration ◽  
Necessary And Sufficient

A bulk M/G/1 system is considered that responds to large increases (decreases) of the queue during the service act by alternating between two service modes. The switching rule is based on two “up” and “down” thresholds for total arrivals over the service act. A necessary and sufficient condition for the ergodicity of a Markov chain embedded into the main queueing process is found. Both complex-analytic and matrix-analytic solutions are obtained for the steady-state distribution. Under the assumption of the same service time distribution in both modes, a combined complex-matrix-analytic method is introduced. The technique of “matrix unfolding” is used, which reduces the problem to a matrix iteration process with the block size much smaller than in the direct application of the matrix-analytic method.

scholarly journals On circulant codes with prescribed distances

1977 ◽  
Vol 16 (3) ◽  
pp. 361-369
Author(s):  
M. Deza ◽  
Peter Eades
Keyword(s):  
Sufficient Conditions ◽  
Difference Sets ◽  
Necessary And Sufficient Conditions ◽  
Necessary Condition ◽  
Weighing Matrices ◽  
Cyclic Difference Sets ◽  
The Matrix ◽  
Circulant Codes ◽  
Necessary And Sufficient ◽  
Square Matrix

Necessary and sufficient conditions are given for a square matrix to te the matrix of distances of a circulant code. These conditions are used to obtain some inequalities for cyclic difference sets, and a necessary condition for the existence of circulant weighing matrices.

Olf-1-binding site: characterization of an olfactory neuron-specific promoter motif

1993 ◽  
Vol 13 (5) ◽  
pp. 3002-3014
Author(s):  
K Kudrycki ◽  
C Stein-Izsak ◽  
C Behn ◽  
M Grillo ◽  
R Akeson ◽  
...  
Keyword(s):  
Nuclear Protein ◽  
Consensus Sequence ◽  
Binding Motif ◽  
Sequence Motif ◽  
Olfactory Neuron ◽  
Sequence Motifs ◽  
Mobility Shift ◽  
Specific Expression ◽  
Mobility Shift Assay

We report characterization of several domains within the 5' flanking region of the olfactory marker protein (OMP) gene that may participate in regulating transcription of this and other olfactory neuron-specific genes. Analysis by electrophoretic mobility shift assay and DNase I footprinting identifies two regions that contain a novel sequence motif. Interactions between this motif and nuclear proteins were detected only with nuclear protein extracts derived from olfactory neuroepithelium, and this activity is more abundant in olfactory epithelium enriched in immature neurons. We have designated a factor(s) involved in this binding as Olf-1. The Olf-1-binding motif consensus sequence was defined as TCCCC(A/T)NGGAG. Studies with transgenic mice indicate that a 0.3-kb fragment of the OMP gene containing one Olf-1 motif is sufficient for olfactory tissue-specific expression of the reporter gene. Some of the other identified sequence motifs also interact specifically with olfactory nuclear protein extracts. We propose that Olf-1 is a novel, olfactory neuron-specific trans-acting factor involved in the cell-specific expression of OMP.

scholarly journals Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila

2018 ◽  
Author(s):  
Doris Bachtrog ◽  
Chris Ellison
Keyword(s):  
Transposable Element ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Binding Sites ◽  
Evolutionary Biology ◽  
De Novo ◽  
Binding Motif ◽  
Sequence Motif ◽  
X Chromosomes ◽  
Msl Complex

The repeatability or predictability of evolution is a central question in evolutionary biology, and most often addressed in experimental evolution studies. Here, we infer how genetically heterogeneous natural systems acquire the same molecular changes, to address how genomic background affects adaptation in natural populations. In particular, we take advantage of independently formed neo-sex chromosomes in Drosophila species that have evolved dosage compensation by co-opting the dosage compensation (MSL) complex, to study the mutational paths that have led to the acquisition of 100s of novel binding sites for the MSL complex in different species. This complex recognizes a conserved 21-bp GA-rich sequence motif that is enriched on the X chromosome, and newly formed X chromosomes recruit the MSL complex by de novo acquisition of this binding motif. We identify recently formed sex chromosomes in the Drosophila repleta and robusta species groups by genome sequencing, and generate genomic occupancy maps of the MSL complex to infer the location of novel binding sites. We find that diverse mutational paths were utilized in each species to evolve 100s of de novo binding motifs along the neo-X, including expansions of microsatellites and transposable element insertions. However, the propensity to utilize a particular mutational path differs between independently formed X chromosomes, and appears to be contingent on genomic properties of that species, such as simple repeat or transposable element density. This establishes the “genomic environment” as an important determinant in predicting the outcome of evolutionary adaptations.

scholarly journals On Solutions of the Matrix Equation A ∘ l X  = B with respect to M M -2 Semitensor Product

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Jin Wang
Keyword(s):  
Matrix Equation ◽  
Matrix Multiplication ◽  
Sufficient Condition ◽  
Mathematical Tool ◽  
Necessary And Sufficient Condition ◽  
The Matrix ◽  
Necessary And Sufficient

M M -2 semitensor product is a new and very useful mathematical tool, which breaks the limitation of traditional matrix multiplication on the dimension of matrices and has a wide application prospect. This article aims to investigate the solutions of the matrix equation A ° l X = B with respect to M M -2 semitensor product. The case where the solutions of the equation are vectors is discussed first. Compatible conditions of matrices and the necessary and sufficient condition for the solvability is studied successively. Furthermore, concrete methods of solving the equation are provided. Then, the case where the solutions of the equation are matrices is studied in a similar way. Finally, several examples are given to illustrate the efficiency of the results.

The algebra of differential forms on a full matric bialgebra

1993 ◽  
Vol 114 (1) ◽  
pp. 111-130 ◽  
Author(s):  
A. Sudbery
Keyword(s):  
Vector Space ◽  
Commutative Algebra ◽  
Differential Algebra ◽  
Differential Forms ◽  
Sufficient Conditions ◽  
Classical Case ◽  
Algebra Of Functions ◽  
The Matrix ◽  
Constant Coefficients ◽  
Necessary And Sufficient

AbstractWe construct a non-commutative analogue of the algebra of differential forms on the space of endomorphisms of a vector space, given a non-commutative algebra of functions and differential forms on the vector space. The construction yields a differential bialgebra which is a skew product of an algebra of functions and an algebra of differential forms with constant coefficients. We give necessary and sufficient conditions for such an algebra to exist, show that it is uniquely determined by the differential algebra on the vector space, and show that it is a non-commutative superpolynomial algebra in the matrix elements and their differentials (i.e. that it has the same dimensions of homogeneous components as in the classical case).

On the factorable spaces of absolutely p-summable, null, convergent, and bounded sequences

2021 ◽  
Vol 71 (6) ◽  
pp. 1375-1400
Author(s):  
Feyzi Başar ◽  
Hadi Roopaei
Keyword(s):  
Lower Bound ◽  
Sequence Space ◽  
Sufficient Conditions ◽  
Necessary And Sufficient Conditions ◽  
Matrix Transformations ◽  
Infinite Matrix ◽  
The Matrix ◽  
Alpha Beta ◽  
Necessary And Sufficient ◽  
Bounded Sequences

Abstract Let F denote the factorable matrix and X ∈ {ℓp , c 0, c, ℓ ∞}. In this study, we introduce the domains X(F) of the factorable matrix in the spaces X. Also, we give the bases and determine the alpha-, beta- and gamma-duals of the spaces X(F). We obtain the necessary and sufficient conditions on an infinite matrix belonging to the classes (ℓ p (F), ℓ ∞), (ℓ p (F), f) and (X, Y(F)) of matrix transformations, where Y denotes any given sequence space. Furthermore, we give the necessary and sufficient conditions for factorizing an operator based on the matrix F and derive two factorizations for the Cesàro and Hilbert matrices based on the Gamma matrix. Additionally, we investigate the norm of operators on the domain of the matrix F. Finally, we find the norm of Hilbert operators on some sequence spaces and deal with the lower bound of operators on the domain of the factorable matrix.

Sequences controlling transcription of the Chlamydomonas reinhardtii beta 2-tubulin gene after deflagellation and during the cell cycle

1994 ◽  
Vol 14 (8) ◽  
pp. 5165-5174
Author(s):  
J P Davies ◽  
A R Grossman
Keyword(s):  
Cell Cycle ◽  
Chlamydomonas Reinhardtii ◽  
Transcription Initiation ◽  
Chimeric Gene ◽  
Transcriptional Level ◽  
Sequence Motif ◽  
Tubulin Gene ◽  
Rich Region ◽  
Beta 2 ◽  
Encoding Genes

In Chlamydomonas reinhardtii, transcripts from the beta 2-tubulin gene (tubB2), as well as those from other tubulin-encoding genes, accumulate immediately after flagellar excision as well as at a specific time in the cell cycle. Control of tubB2 transcript accumulation following deflagellation is regulated, at least partially, at the transcriptional level. We have fused the tubB2 promoter to the arylsulfatase (ars) reporter gene, introduced this construct into C. reinhardtii, and compared expression of the chimeric gene with that of the endogenous tubB2 gene. After flagellar excision, transcripts from the tubB2/ars chimeric gene accumulate with kinetics similar to those of transcripts from the endogenous tubB2 gene. The tubB2/ars transcripts also accumulate in a cell cycle-specific manner; however, chimeric transcripts are more abundant earlier in the cell cycle than the endogenous tubB2 transcripts. To elucidate transcriptional control of tubB2, we have mutated or removed sequences in the tubB2 promoter and examined the effect on transcription. The tubB2 promoter shares features with the promoters of other tubulin-encoding genes; these include a GC-rich region between the TATA box and the transcription initiation site and multiple copies of a 10-bp sequence motif that we call the tub box. The tubB2 gene contains seven tub box motifs. Changing the GC-rich region to an AT-rich region or removing three of the seven tub box motifs did not significantly affect transcription of the chimeric gene. However, removing four or five tub box motifs prevented increased transcription following deflagellation and diminished cell cycle-regulated transcription from the tubB2 promoter.

Orthonormal Isotropic Vector Bases

1998 ◽  
Author(s):  
Namik Ciblak ◽  
Harvey Lipkin
Keyword(s):  
Recursive Algorithm ◽  
Computer Applications ◽  
Sufficient Condition ◽  
Necessary And Sufficient Condition ◽  
Orthonormal Bases ◽  
Isotropic Vector ◽  
The Matrix ◽  
Necessary And Sufficient ◽  
Deviatoric Stresses ◽  
Isotropic Vectors

Abstract Orthonormal bases of isotropic vectors for indefinite square matrices are proposed and solved. A necessary and sufficient condition is that the matrix must have zero trace. A recursive algorithm is presented for computer applications. The isotropic vectors of 3 × 3 matrices are solved explicitly. Deviatoric stresses in continuum mechanics, the existence of isotropic vectors (particularly in screw space), and stiffness synthesis by springs are shown to be related to the isotropic vector problem.

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