UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 5)*

Calyxt, Inc.

(Name of Issuer)

Common Stock, par value $0.0001 per share

(Title of Class of Securities)

13173L107

(CUSIP Number)

Marie-Bleuenn Terrier

General Counsel

Cellectis S.A.

8, rue de la Croix Jarry

75013 Paris, France

+33 1 81 69 16 00

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

October 31, 2022

(Date of Event Which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition which is the subject of this Schedule 13D, and is filing this schedule because of §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box:  ☐

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See Rule 13d-7 for other parties to whom copies are to be sent.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

Explanatory Note

This Amendment No. 5 (this “Amendment No. 5”) amends and supplements the Schedule 13D of Cellectis S.A. (the “Reporting Person”) initially filed with the SEC on May 29, 2018, as amended by Amendment No. 1 thereto filed on June 15, 2018, Amendment No. 2 thereto filed on September 23, 2019, Amendment No. 3 thereto filed on July 9, 2020 and Amendment No. 4 thereto (“Amendment No. 4”) filed on October 23, 2020 (as so amended, the “Schedule 13D”). Capitalized terms used herein and not defined herein have the meanings ascribed thereto in the Schedule 13D.

This Amendment No. 5 is being filed by the Reporting Person to report: (i) an update of the beneficial ownership percentage of the Reporting Person resulting solely from an increase in the number of outstanding shares of the Company’s Common Stock, (ii) changes in disclosure responsive to Items 4 and 6 of the Schedule 13D, as set forth below, and (iii) certain changes to the directors and executive officers of the Reporting Person, as set forth in Schedule A hereto.

Except as specifically provided herein, this Amendment No. 5 does not modify or amend any of the information previously reported in the Schedule 13D. Items that have been supplemented provide additional, supplemental information to the information reported in the Schedule 13D and do not supersede such existing information.

Item 2. Identity and Background

Item 2 (a) – (f) is hereby amended and supplemented with respect to each executive officer and director of the Reporting Person as follows:

The name, business address, present principal occupation or employment (and address of any corporation or other organization in which such employment is conducted) and citizenship of each director and executive officer of the Reporting Person is set forth on Schedule A to this Amendment No. 5.

During the last five years, neither the Reporting Person nor, to the knowledge of the Reporting Person, any of the persons listed on Schedule A to this Amendment No. 5, (i) has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors) or (ii) was a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding was or is subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

Item 4. Purpose of Transaction.

Item 4 is hereby amended and restated in its entirety as follows:

The Reporting Person has acquired and holds Common Stock of the Company for the Reporting Person’s investment purposes. The information set forth under Item 6 of this Schedule 13D is incorporated herein by reference.

During the period in which the Reporting Person held more than 50% of the voting power and more than a majority of the outstanding Common Stock of the Company, the Company was a “Controlled Company,” as defined in Rule 5615(c)(2) of the rules of the NASDAQ Stock Market LLC (the “NASDAQ”). On October 31, 2022, the Company provided the Reporting Person with the number of outstanding shares of Common Stock (48,815,376 shares) as of October 28, 2022. Based on this number of outstanding shares of Common Stock, the Reporting Person no longer holds a majority of the outstanding Common Stock of the Company and the Company is no longer a “Controlled Company.”

The Reporting Person is party to a stockholders agreement dated July 25, 2017 with the Company (as amended from time to time, the “Stockholders Agreement”), which provides the Reporting Person with contractual rights to approve specified corporate actions of the Company. As a result of the foregoing, the Reporting Person has the ability to determine the outcome of various matters. In particular, the Reporting Person has certain approval rights for so long as the Reporting Person beneficially owns at least 15% of the then outstanding shares of the Company’s Common Stock with respect to several enumerated items.

Among such rights granted under the Stockholders Agreement, the Reporting Person is entitled to nominate the greater of three members of the Company’s Board of Directors or a majority of the directors, to designated the Chairman of the Reporting Person’s Board of Directors, and to designate one member to each of the audit committee of the board of directors, the compensation committee of the board of directors and the nominating and corporation governance committee of the board of directors of the Company. In accordance with the terms of the Stockholders Agreement, the Reporting Person has previously appointed Laurent Arthaud, a member of the Reporting Person’s Board of Directors, as a member of the board of directors of the Company, including as a member of the compensation committee and the nominating and corporate governance committee of the Company’s board of

directors. The Reporting Person has reserved, but not exercised, all other board of directors designation rights under the Stockholders Agreement. The Reporting Person acknowledges that, subject to the “phase-in” periods permitted by NASDAQ for companies that cease to be “Controlled Companies,” the Company is required to comply with the NASDAQ’s independence requirements applicable to the compensation committee and the nominating and corporate governance committee of the Company’s board of directors.

In its capacity as a significant stockholder of the Company and beneficiary of certain approval rights pursuant to the Stockholders Agreement, the Reporting Person intends, from time to time, to engage in discussions with the board of directors of the Company and/or members of the Company’s management team concerning a broad range of operational, financial and strategic matters, including, without limitation, the Company’s business, operations, capital structure, governance, management, and strategy as well as potential financings, business combinations, strategic alternatives (including those which may arise as a result of the Company’s previously announced evaluation by the Company’s board of directors of a full range of strategic alternatives), and other matters concerning the Company. The Reporting Person may communicate with other stockholders or third parties regarding the foregoing.

On an ongoing basis, the Reporting Person will review the Company’s operating, management, business affairs, capital needs and general industry and economic conditions, and, based on such review, the Reporting Person may, from time to time, determine to increase or decrease its ownership of Common Stock, exercise, withhold or waive its required approval pursuant to the Stockholders Agreement, or vote to approve an extraordinary corporate transaction with regard to the Company.

The Reporting Person has in the past approved the Company’s capital markets financing activities, including the Company’s at-the-market financing program, and intends to evaluate and, where appropriate in respect of the Company’s liquidity needs, approve further financing transactions that may be presented for approval.

In addition, the Reporting Person intends to take such actions as may be requested by the Company in connection with the implementation of the reverse stock split approved at the Company’s 2022 annual meeting for purposes of curing any deficiency in the Company’s compliance with applicable NASDAQ listing requirements.

Except as otherwise described in this Item 4 of Schedule 13D, the Reporting Person does not have any present plans or proposals which relate to or which would result in the types of events described in clauses (a) through (j) under Item 4 of Schedule 13D.

Item 5. Interest in Securities of the Issuer

Item 5(a) – (c) is hereby amended and supplemented as follows:

(a) – (c) The Reporting Person beneficially owns 23,963,175 shares of Common Stock, representing 49.1% of the outstanding Common Stock of the Company. The percentage of beneficial ownership of the Reporting Person is based upon 48,815,376 shares of Common Stock of the Company outstanding as of October 28, 2022.

At the time of the filing of Amendment No. 4 to the Reporting Person’s Schedule 13D on October 23, 2020, the shares of Common Stock beneficially owned by the Reporting Person represented 64.7% of the outstanding Common Stock of the Company.

Since the filing of Amendment No. 4, the Reporting Person has not effected any transactions in the Company’s Common Stock or other securities.

Following Amendment No. 4, the Reporting Person’s beneficial ownership percentage has changed resulting solely from an increase in the number of outstanding shares of the Company’s Common Stock. Based on information disclosed in the Company’s periodic reports filed with the Securities and Exchange Commission subsequent to the filing of Amendment No. 4:

The Reporting Person possesses sole power to vote and sole power to dispose of all the shares of Common Stock beneficially owned by the Reporting Person.

Item 6. Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer

Item 6 is hereby supplemented as follows:

As of the date of this report, the Reporting Person and its affiliates no longer hold a majority of the Company’s outstanding shares of Common Stock.

Pursuant to the Stockholders Agreement, certain matters with respect to the Company require the Reporting Person’s prior approval for so long as it beneficially owns at least 15% of the then outstanding shares of the Company’s Common Stock, including the right to approve:

Further, pursuant to the Stockholders Agreement, until the first date on which the Reporting Person and its affiliates no longer beneficially own at least 15% of the outstanding shares of the Company’s Common Stock, the Reporting Person has the right to designate the greater of three members of the board of directors or a majority of the directors on the board of directors, and to designate the chairman of the board of directors and one member to each committee of the board of directors of the Company.

The description of the Stockholders Agreement contained in the Schedule 13D, as supplemented by this Amendment No. 5, is only a summary and is qualified in its entirety by reference to the full text of the Stockholders Agreement, a copy of which is filed as Exhibits 1 and 2 to Schedule 13D filed by the Reporting Person on May 17, 2018, and incorporated herein by reference.

Signature

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Dated: November 1, 2022

SCHEDULE A

CERTAIN INFORMATION CONCERNING EXECUTIVE OFFICERS AND DIRECTORS OF

CELLECTIS S.A.

The following table sets forth name, business address, present principal occupation or employment (and address of any corporation or other organization in which such employment is conducted) and citizenship of each director and executive officer of the Reporting Person. The current business address for Cellectis S.A. and, except as otherwise noted, for each person identified in this Schedule A is c/o Cellectis S.A., 8, rue de la Croix Jarry 75013 Paris, France and the telephone number is +33 (0)1 81 69 16 00.

Directors